Buggy code:
Hashtable < String , Annotations > Annos ; Hashtable < String , Annotations > Externals ; FastaReader rr ; Annotations Ref ; Annotations Cyto ; double bpp ; int window_width ; String PvarID = null ; Annotations Pvar = null ; Element Ele_var = null ; Annotations Panno = null ; Element [ ] Ele_anno = null ; Annotations Pfanno = null ; Element Ele_fanno = null ; Hashtable < String , Annotations > Pclns = new Hashtable < String , Annotations > ( ) ; IndividualStat is = null ; String scoremeth = null ; public Instance ( ) { } public Instance ( String Assembly ) { } void initialize ( String Assembly ) { } public String refresh ( String chr , long start , long end , int window_width ) { } public String update ( String chr , long start , long end , int window_width ) { } public String add_Tracks ( String [ ] tracks , String [ ] modes ) { } public void remove_Tracks ( String [ ] tracks ) { } public void add_Externals ( String [ ] tracks , String [ ] links , String [ ] types , String [ ] modes ) { } public void add_ExIndividuals ( String [ ] tracks , String [ ] links , String [ ] types , String [ ] modes ) { } public void remove_Externals ( String [ ] tracks ) { } public void init_Pvar ( String track , String PvarID ) { } private void init_IndividualStat ( ) { } public String add_Pvar ( String track , String mode , String PvarID ) { } public void remove_Pvar ( ) { } public String add_Panno ( String track , String mode ) { } public void remove_Panno ( ) { } public String add_Pfanno ( String track , String mode ) { } public String remove_Pfanno ( ) { } public String add_Pclns ( String [ ] tracks , String [ ] modes ) { } public void remove_Pclns ( String [ ] tracks ) { } public String get_Detail ( String trackname_in , String id , int start , int end ) { } public String get_Geneinfo ( String gene ) { } public String find_Gene ( String prefix ) { } public String get_OverlapGenes ( String chr , int start , int end ) { } public String get_RankingGenes ( int top_number ) { } public String get_Assemblies ( ) { } public String get_Chromosomes ( ) { } public String get_Cyto ( String chr ) { } public String get_Cyto ( ) { } public String get_SingleCytoScore ( String chr , String id ) { } public String get_Ped ( String track ) { } public String prioritize_Individuals ( String track , String vcfs ) { } public String get_LinkageDisequilibrium ( String track , String id , long start , long end ) { } public String get_Intersection ( String track , String set_a , String chr , long start , long end ) { } public String get_TrioAnalysis ( String track , String id , String chr , long start , long end ) { Document doc = XmlWriter . init ( DATA_ROOT ) ; int chrid = check_chromosome ( chr ) ; if ( chrid >= 0 ) { Annotations vt = null ; if ( Externals . containsKey ( track ) ) vt = Externals . get ( track ) ; else if ( Annos . containsKey ( track ) ) vt = Annos . get ( track ) ; else if ( ( ( ( Pvar ) != null ) && ( track . startsWith ( "_" ) ) ) && ( track . substring ( 1 ) . equals ( Pvar . get_ID ( ) ) ) ) vt = Pvar ; if ( ( ( vt != null ) && ( vt . get_Type ( ) . equals ( FORMAT_VCF ) ) ) && ( vt . has_Parameter ( Consts . VCF_HEADER_SAMPLE ) ) ) { VcfReader vr = new VcfReader ( vt , chr ) ; <START_BUG> Element [ ] ele_temp = vr . write_trio ( doc , id , chr , start , end , false ) ; <END_BUG> } } return XmlWriter . xml2string ( doc ) ; } public String get_Difference ( String track , String set_a , String set_b , String chr , long start , long end ) { } public void remove_Ped ( String track ) { } public void add_Ped ( String track , String ped ) { } public void load_Ped ( String track , String filepath ) { } public void load_Stat ( String filepath ) { } public String save_Stat ( String session ) { } public String set_ScoreMethod ( String scoremeth ) { } public String get_ScoreMethod ( ) { } public String get_Annotations ( ) { } public String get_Externals ( ) { } public String get_Check ( String trackname ) { } public String get_CheckValue ( String trackname ) { } public String get_Individuals ( ) { } public String get_ExIndividuals ( ) { } public String get_Parameters ( String [ ] tracks ) { } public void set_Params ( String [ ] tracks , String [ ] params , String [ ] values ) { } public void save_Index ( String trackname , String session ) { } void set_mode ( String track , String mode ) { } void append_Ptrack ( Annotations track , Document doc , String mode , int Class ) { } void init_track ( Annotations track ) { } void append_track ( Annotations track , Document doc , String mode ) { } void add_att_ifParam ( Annotations track , Element ele_temp ) { } int check_chromosome ( String chr ) { } long [ ] check_coordinate ( int chr_info , long start , long end ) { } Annotations [ ] get_BasicAnnos ( ) { }

Fix:
Element [ ] ele_temp = vr . write_trio ( doc , id , chr , start , end , false , false ) ;